Beamline 4.2.2 Operating Instructions
Contents
1. Figure 1 2 NX Client Connection Wizard 1 1 2 Advanced Configuration If you are using the NX Client on Windows XP you may skip to subsection 1 1 3 as the Advanced Configu ration options only apply to Linux and OSX operating systems NOMAGHIN Advanced Services Environment About Server Host 128 3 220 35 Port 22 Remember my password O e check Use custom settings Settings ADSL WAN LAN e press ATTE Display w 1280 H 1024 M Use custom settings gt Settings Figure 1 3 NX Client Advanced Configuration Images Use both JPEG and RGE compression O p O Only use JPEG compression Only use RGB compression Use plain X bitmaps Quality Use custom JPEG quality y 01234567809 e select Use plain X bitmaps p etaman e save Advanced Configuration settings Disable the render extension Disable the backing store Disable the composite extension Disable the shared memory extension Disable emulation of shared pixmaps Figure 1 4 NX Client Custom Settings 1 1 3 Connect to Berkeley NOMAGHINE Password e run the NX Client and login Session RemoteCollectionALS422 a Login as a guest user GHD Core e Welcome to Berkeley Figure 1 5 NX Client Connect to Host Chapter 2 Running the Beamline The majority of beamline operations are controlled through the MBC User menu right click the Desktop MBC USER2. ___ Robot Commands Mounted Pin Busy Dry Soak Wait Anneal Puck Pa Pin EH Dismount Emor m Pin Selector gt Msg Dewar Commands E E E Location ROBOT_LOCATION_WAIT Open Close Automation 0609009 E Q O 0 a Low Res Sample Hi Res 00000 gt are y Ss 0 10 e 10 6 10 4 10 6 10 Set Omega OOOO Haml Soo oe 08 Jun 2009 18 33 50 NOTE Move of motor gonio_phi completed normally at 19 9890478279 J y Idle Energy 12397 86 eV Master Active Shutter Closed 06 34 29 PM Figure 2 6 BLU ICE ROBOT TAB Setup for Use The ROBOT tab is used for mounting centering exchange or dismounting of crystals Prior to any use it is important to wake the robot and put the goniometer cryo stream beamstop and detector into mounting position These events are all triggered by the Setup for Use button Initialize Initialize updates the status of BLU ICE with the robot control computer and ensures all values are current As with all robot commands initialization must be done after Setup for Use is pushed It never hurts to initialize but it is absolutely necessary if one starts restarts BLU ICE with a crystal mounted Robot Commands tritio CC Dry Soak Wait Anneal Dewar Commands 1 press AUTOMATION gt Setup for Use Open Close 2 press ROBOT COMMANDS gt Initialize Automation set
3. Figure 2 11 BLU ICE New Run 13 2 33 The Hutch Tab Phi Start Cancel Stop ol 19 989 y deg a Pata Two Theta Beam Size 0 000 w deg Automation Sample Low Res Sample Hi Res A Resolution Predictor Position Sample Set Omega 4 A wt I 5 y OA E weak i m ae o Y Eare Detector Radius 80 v mm 08 Jun 2009 18 33 50 NOTE Move of motor gonio_phi completed normally at 19 9890478279 y Idle Energy 12397 86 eV Master Active Shutter Closed 06 34 04 PM Figure 2 12 BLU ICE HUTCH TAB The hutch tab can be used to set detector distance omega angle phi angle and slits The following are instructions on the two most common uses setting phi angle and slits width Adjusting the phi angle is often used to flip the crystal when collecting the second 180 of a 360 collection Changing the slits opening is often performed when the crystal is much smaller than the beam and one wishes to minimize air scatter Note that there is also a proportional loss of flux onto the sample Setting the Phi Angle e choose PHI gt angle from the drop down e g 180 to shoot the backside of the crystal 14 Setting the Slits in BEAM SIZE WIDTH number between 0 05 mm and 0 70 mm press Start HEIGHT number Positive between 0 05 mm and 1 00 mm NEVER enter a negative number press Start 15 2 3 4 The Setup Tab File Component Sh
4. The opposing button is downward movement The adjacent pair move orthogonal to the video screen The fos ENS and HEN buttons rotate Omega to that angle The bottom pair of ES and E buttons move left lt and right on the video feed The il menu reset if the widget locks up home moves everything back to the mounting position Exchange or Dismount a Crystal e press AUTOMATION gt Setup for Use e press CENTERING WIDGET gt Ki Home e To Exchange choose the next pin to mount press NEXT PIN gt Mount The robot begins the Dismount Exchange and Mount process e To Dismount press MOUNTED PIN gt Dismount 11 2 3 File 2 The Collection Tab Component Shutter Master View Options Hutch Collect Scan Setup Robot gt gt e EEE dad do oda dio de e filer Data daly reference image QQ o o s o s uv a a i a weer eer eer eee ewe o o lt owner re eee er o e e ARANA 441444544444 777 EE ee EE EE EE E E 6444444444464 eee ee ee AA 4444464444444 Collect Current Position 4 WAY WY HY LET Hy AA Phi Hy AY Omega Kappa Distance Abort 19 99 180 00 0 00 350 00 Collect Start
5. e choose Konsole e type user ACTION SAMPLE e The MBC User menu loads Figure 2 1 MBC USER The ACQUISITION submenu has four tools for data collection Data Acquisition Monitor Filters BLU ICE and Tune Optimize Figure 2 2 shows a remote desktop session with all four tools Each section of this chapter is dedicated to one of the tools with sections ordered as they appear in the ACQUISITION submenu The Center Widget which is also shown in Figure 2 2 is opened by typing center in a new Konsole and is addressed in subsection 2 3 1 of BLU ICE r ss Y BEAMLINE 4 2 2 Version R 2 3 X Y ShutterFilter ad MBC USER iv optimizeTune adl XA NewNoirMonitorScreen ad x 120000 100000 Omega Angle 0 000 r AN Omega Delta 1 00 ACTION SAMPLE ACQUI 60000 xposure 1000 neta BLU ICE EPICS MBC ALS Beamline 422 nae Energy 12397 821 Distance 97001 ay Program Gonio Sync Master Resp ok Cd Qe 20000 Phi Stop al State vaitComand waitComand Status MIME MA m Hi E a A a 7 US Distance 4 Shutt CA FWHM urad MAX urad j Counts TUNE urad Step Pts Integrate Fix Stored Image C e599x3 4_1805 mi eneriy Width Height x a ao sal ail res97 02 yiev 0 55 y mm x 0 20 mm a Beamstop Two Theta Reval Eas File Name e599x3_1 180 r Beam Size 0 000 y mm 0 000 deg Start Scan A Program Z p
6. mi E 2 __ Abort Scan a waitCommand Automation Sample Low Res Sample Hi Res Resolution Predictor Ta Bei a Errors SUCCESS STORE Access Sample Position Sample p I E Use Sample So e Optimize Beam Al x 257A Set Omega y oj soj 100 fc Detector Radius 80 y mm Z Translation E Pa E gt z5 17 Jun 2009 14 24 47 NOTE Move of motor gonio_omega completed normally at 7 65845734742e 05 a ENE o de o Energy 12397 82 eV Master Active Shutter Closed 02 25 14 PM Reset E Hone 7 O amp ip ldkcessir X BEAMLINE4 2 2 Version XX BLU ICE EPICS MBC AL X Medm 8 on aor Displaycessir X iceR23VideoPitch tcl Shell Konsole 4 a 2009 06 17 Figure 2 2 Remote Session 2 1 Data Acquisition Monitor The Data Acquisition Monitor also known as the Data Collection Monitor is shown on the right side of Figure 2 2 It provides real time information on the status of data collection including ccd status detector position shutter open close path of last image taken and image name Of note is a window that lists error messages if a new message goes into the box contact beamline support to continue 2 2 Filters The beamline filters are various metal foils which are used to attenuate the beam The attenuation factor of each is filter is energy dependent and the best way to determine the appropriate filter is to activate one or more until t
7. Angle Example 001 0 00 e RUN TYPE choose Dark Still if you don t have a dark image for that amount of time choose Still if the last image you took was for the same amount of time e click Collect Collect a Dataset When collecting a dataset it is important to note that you can only collect on Omega between 0 and 180 If you need to collect more collect the first 180 with Omega flip the crystal 180 in Phi and collect with Omega between 0 and 180 again for the back side e press the TAB to create a new run e Follow Collect a Still Image but notice the availability of END Frame Number Omega Angle 1 enter the START Frame Omega 2 enter the END Omega 3 END Frame will auto fill e Dark Images are collected automatically e click Collect e click Reset if the run stops early When re inputing the Frame Number and Omega Angle subsequent to a re set be sure not to press enter following the Frame Number Doing so will pre vent BLU ICE from properly resuming the data collection Only press enter after inputing the Omega Angle e Default U date Delete L i p Bia File Prefix qoodxtal Run 1 inactive Directory fusertffoome Model 22 Fast Distance 150 000 mm Axis gonio_omega Delta 1 00 deq Time 105 Relative Dose 1 00 Frame gonio omega Start 001 0 00 deg End 180 180 00 deg Ej Wedge 180 0 deg Energy 12397 86 eV ev
8. Beamline 4 2 2 Operating Instructions the Molecular Biology Consortium http mbc als org latest version link July 9 2009 Contents 1 Remote Access El NOG ot Sar eae caro ie Gh tee ee ee Bs A Sy tee oe ee es e O 1 11 The Connection Wizard ee a s aoe ss w See SSR So see wise eee Sew Sie eo ELZ Advanced COnmeuraviOn za rs aa ad Be Boks bo eee e we eo kko Conner to Berkele ac Aa Ge ee eS Ged i 2 Running the Beamline 2A Data Acquisition Monitor s eii dd Seb ADA OOZES ESS 2E CES cis te cance as at cee ee Se Bee Se A ee Ge Sk A A AU A AA F 2 5 BLUE AS ee BE Be SS AS ER Se A Be ee 2o ICR OO Labra ee as dida ae Rh ee Be He he Bade ere ered aoe a de ee Se e oe Ss SLU Or USO ia amp ak Ge We Ae ate Bea ee es ee A RE a MAIS arca a a AA e rd ew a See a a Mount a Crystal casal As oe AAA E oe Sw g Centersa Cristal arboles Seal aaa add ao Exchange or Dismount a Crystal 2 4 bujia 4 Add e oe oe ety de eS 23 2 The ollection Tab anisz dea chee ke ee eee ee A A BES Colecta tlllmaso so ee amp 4 a ee eS SE A A Collect a Dataset ama i eae Sh E GEO eee ee ee BS Zoo Lhe Uteh baba 24 24 6 4 ae ee ee Oe RES Ee crol settine the PhrAnele ui ed bod aaa ewe eee bE Ewe SLES EEL Os A Me A IA 2 54 Vie Setup Lab 44m sa era a e Pomeroy Ohanes ibi e ps o as dr Boks bo eee SB a O ZA Tune ODUM ura AAA AAA Optimize Bedik esaa A a oe ee A AE EAE HES Wien tO ODONI ad oe sk AA Be eee AA 3 Data Processing Sol Dat
9. Delay min Enable _ Delay Beam 0 Start Run Sequence Help Run 0 inactive 0 Default Update File Prefix foo Directory JuserlAvhoma snap Model 2x2 Fast v Distance 150 000 mm Axis gonio_omega vw Delta 1 00 deg Time 105 Relative Dose 1 00 Frame gonio_omega Start 001 0 00 deg Energy 12397 86 eV E 119 i Hi Run Type 444444 f tf TER y Dark 114143444 tt 1111 v Still gt poe ee Dark Still afi 200 gt 08 Jun 2009 18 33 50 NOTE Move of motor gonio_phi completed normally at 19 9890478279 J y Idle Energy 12397 86 eV Master Active Shutter Closed 06 35 52 PM Figure 2 10 BLU ICE COLLECT TAB The Collection Tab is basically divided in two The left portion displays the current image while the right portion is used to enter the collection values The image display section will update each time a new image is taken and provides some rudimentary controls for viewing the image The image capture section provides all the controls and parameters necessary to collect either a still image or a dataset Collect a Still Image FILE PREFIX Name of your choosing DIRECTORY E g userl awang snap MODE1l 2x2 Fast use default DISTANCE As appropriate 150mm is a good starting point AXIS gonio_omega use default DELTA Is for collection these are true stills TIME Typically 1 3 sec for starters 12 e START Frame Number Omega
10. Table lt ee 17 ATIC OPINIO ura rs e a eee a a ee a a amp Ae doe 18 Chapter 1 Remote Access 1 1 NX Client The NX Client runs graphical desktops and applications across network connections We will be using it in this capacity to remotely access the computer that pilots beamline 4 2 2 e download the client http www nomachine com e install the client for your OS e use the Connection Wizard 1 1 1 The Connection Wizard f NOMACH e SESSION Name of your choosing e Host IP address will be emailed to you e PORT 22 choose Insert name of the session Your configuration settings will be saved with this name Session RemoteCollectionALS422 Insert server s name and port where you want to connect Host 128 3 220 3x Port 22 Select type of your internet connection MODEM ISDN ADSL WAN Figure 1 1 NX Client Connection Wizard Using NX Client you can run RDP VNC and X desktops depending on what the service provider has made available Unix fe KDE Settings e SIZE 1280 x 1024 minimum Select size of your remote desktop w 1280 n 1024 Authorization credentials are always encrypted at the time connection is established To enhance performance you can e choose KDE desktop if it s not the default choose e choose Show Advanced Configuration disable the encryption of the data traffic Disable encryption of all traffic
11. a CORECHONA aare Y a e os amp amp wa Be al E a aa ee dd o eR AAA E ee E A hh a as OA ee ee a oe NMOSEENVE 2 4 sve a A AS aa a Be eS oc AA 3o SINISE BA aa g pe a E A GE ee Aaa a eS Se 0 ADS ca ces eae ar a ds e A See ede tae E a ee i a De ee oR WW O amp Ooo OoONN SO List of Figures LA 12 1 3 1 4 1 5 21 2 2 2 3 2 4 2 0 2 6 2l 2 8 2 9 2 10 2 11 2 12 2 13 2 14 2 15 NX Client Connection Wizard 3 NX Client Connection Wizard 4 NX Client Advanced Configuration Si ie ee era EL sa 4 NX Client Custom De Unesco ds hes ES APRS ee me Be 5 NX Client Connect to Host 5 AO AAA O eo ee OE 6 Remote Sessions oe ee Se Se Bee ae Ye ee Se SEE n AS A 7 BLU ICE Starting BLU ICE 3 ide d de Oe amp mom ee husk he Se do Se e de te 8 BEUIGES lt Functionality labs a e g s naaa a aana LEE Aa E a a 8 BEUAICE ROBOT TAB avale di ede ra a a a eet a Y e ea 9 BLUEICE Setup or Use alias ir SRE AA EE MAO eEE Se Cees 10 BLU ICE Pin SelectOrs s 2 4 4 454 4 4 44 cada bt hae wWe hb ew a a oS 10 Center Widget si ars e ed bbb ot eee EES eee Bee be ne GSS i 11 BEU ICE COLLECT LAB 6 4 sack E Ae eee Be ee Soe Wie ee SE a 12 BLUEICE New lle vetas oe eed es Se SBS SoS A ae Bee ed 13 eh RO POM LAB i on ewes sio de tes ie E de ee Cb ha a Se OO AS 14 BLUSICE SETUP TAB ae es aah eve Be Ge eck a See Be ee eS S 16 BLU ICE Tune Entries
12. he beam is attenuated the desired amount based on a snapshot ShutterFilter adl EZS A Figure 2 3 Filters 2 3 BLU ICE BLU ICE is a widely used graphical user interface for crystallography According to BLU ICE development team the highly graphical BLU ICE user interface simplifies sophisticated experimental protocols and complex motor relationships hides the complexities of the control and computer infrastructure and allows the user to concentrate on the problem at hand the collection of diffraction data or the maintenance of a beamline It is important to note however that beamline 4 2 2 runs on a customized version of BLU ICE that integrates with the EPICS control system As such the most relevant information for using BLU ICE at beamline 4 2 2 is contained within this document MBC USER ACTION SAMPLE o choose ACQUISITION Blu Ice Data Acquisition Monitor FILTERS Blu Ice Tune Optimize Figure 2 4 BLU ICE Starting BLU ICE e notice the 5 functionality tabs File Component Shutter Master View Options Hutch Collect Scan Setup Robot Figure 2 5 BLU ICE 5 Functionality Tabs e choose the ROBOT tab from Introduction to BLU ICE and DCS at http smb slac stanford edu research developments blu ice intro html 2 3 1 The Robot Tab File Component Shutter Master View Options Help Hutch 7 Collect Scan Setup Robot Next Pin Robot Status
13. nt to note that your processing directory must reside within your home directory as data directories do not have write permissions for processing Please create a processing directory for the dataset you would like to work on 3 1 Data Correction e cp scripts correct com to copy correct com to your home directory e edit correct com for the month year e g aug09 and login name see example script e run correct com on a directory containing the data this will correct all the contents of that directory e g csh correct com x2Bsure 3 2 d TREK e cd to the processing directory e type dtdisplay path to image tab completion works wonders here e g dtdisplay user1 awesomeuser snap xtal_0_001 e alternately type dtdisplay then file gt open and navigate to the image in the GUI select process dtprocess from the display menu e the user manual http pdfs mbc als org dtrek_overview99 pdf 19 3 3 HKL2000 e cd to the processing directory e type HKL2000 e the user manual http www hkl xray com 3 4 MOSFLM e cd to the processing directory e cp scripts start inp to current directory e edit start inp for image name and path e type mosflm lt start inp 3 5 IMOSFLM e cd to the processing directory e type imosflm e use GUI to open images and process 3 6 XDS Information on installation and use of XDS http xds mpimf heidelberg mpg de 20
14. quence called Optimize Beam from HUTCH TAB gt AUTOMATION gt Optimize Beam The sequence works as follows 100000 1 The sample is moved out of the beam 2 The shutter opens and the scan begins e TUNE OPTIMIZE plots the beam intensity vs the second crystal position 3 The scan completes and the shutter closes FWHM Curad HAK Curad 4 The sample is returned to the original position Counts TUNE urad 5 The tune motors are moved to maximum flux Sten T ate Se A000 E 1 0 100 H a 6 If TUNE OPTIMIZE doesn t show a peak click Ma Scanning Active Optimize Beam again Tune Enabled SSS Figure 2 15 Tune Optimize When to Optimize Beam optimization may be done any time a run is not in progress It was very popular after a beam fill when the ALS was running in Decay Mode however Top Off Mode keeps the optics at a constant temperature That said it doesn t hurt to optimize often One popular practice is to start a beam optimization before collecting a dataset filling in collection values while the beam is optimizing Collection may proceed once optimization is complete 18 Chapter 3 Data Processing Data processing at beamline 4 2 2 can be done using e d TREK e HKL2000 e MOSFLM e XDS All of the above programs can process corrected images d TREK can also process raw images that it corrects on the fly making it convenient to process while still collecting When processing data it is importa
15. s beamtime In order to provide the maximum flexibility for the experimenter we have devised a simple lookup table which allows the user to choose specific energies for collection Any energy from 5 500eV to 15 500eV can be made available Users that wish to change energies are encouraged to let staff know prior to beamtime so that the lookup table and energies may be optimized during startup and tune 16 Energy Changes Tune Entries Energy Tune 7500 02 44 929 8175 01 33 406 12388 11 38 286 12397 99 41 620 12664 87 45 660 Twist 62 987 55 260 1 845 2 251 3 904 Focus Roll 1 398 3 904 3 920 4 056 13574 99 70578 17 867 4 526 Figure 2 14 BLU ICE Tune Entries Table 0 070 0 044 0 067 Pitch Date Entered 4 493 4 494 4 493 4 495 4 495 4 498 2009 05 19 12 50 46 2009 05 22 15 07 38 2009 05 27 11 04 35 2009 05 27 15 05 28 2009 05 22 21 33 26 2009 05 19 12 46 56 17 choose View gt Show Tune Entries the Tune Entries table appears the left column shows available energies click on the desired energy click the HUTCH TAB click AUTOMATION Optimize Beam click the COLLECT TAB click RUN gt ENERGY now reflects the change 2 4 Tune Optimize Optimize Beam Flux at the sample is maximized when the first and second crystals of the monochromator are paral lel To achieve this we run a se
16. up For Use Figure 2 7 BLU ICE Setup for Use Mount a Crystal The PIN SELECTOR field has 5 columns and 12 rows Columns represent pucks in the robot s dewar while rows are pin positions within each puck Thus 4 2 indicates puck 4 pin position 2 Next Pin e press Setup for Use Puck 4 Pin 2 Mount e press D home Mounted Pin e click the desired Pin in PIN SELECTOR Puck 4 Pin Dismount e NEXT PIN will reflect the choice Pin Selector e press NEXT PIN gt Mount 1 21 G 51 e The robot begins the mounting procedure Do not press any buttons during the gt 22 2 B execution of the command A in the ROBOT STATUS gt fot PAN A A ai Busy represents activity Mount is complete when the black bor der appears in the centering widget Figure 2 8 BLU ICE Pin Selector 10 Center a Crystal AY Slide O00 Tranz lation oo gt Pos Toon Reset g Home Figure 2 9 Center Widget The crystal is mounted on a 6 stage goniometer e choose the HIGH Res tab of the video feed e open a new Konsole type center e The CENTER WIDGET will open The left numerical column is requested position The right numerical column is actual position The upper quadrangle governs movement based on the Omega angle buttons are paired by row The four E and E buttons are directional movement The black border always halos upward movement
17. utter Master View Options Help Hutch Collect Scan Setup Robot Move by Move to Undo Move Selected Motor Abort Scan Configure Yi 0 10 M en Ea E Tame Entries EA Tune Twist Focus Roll Pitch Date Entered 7500 02 A aan menaa 44 929 62 987 0 998 0 080 4 493 2009 05 19 12 50 46 75 01 A 33 406 55 260 1 398 0 070 4 494 2009 05 22 15 07 38 3 904 0 044 4 493 2009 05 27 11 04 35 81 12388 11 en aan nae am aen aan me 286 12397 99 OR 620 2 251 12664 87 CO 45 660 3 904 4 056 0 067 4 495 2009 05 22 21 33 26 3 920 0 060 4 495 2009 05 27 15 05 28 13574 99 zz 578 17 867 4526 0 056 4 498 2009 05 19 12 46 56 08 Jun 2009 18 33 50 NOTE Move of motor gonio_phi completed normally at 19 9890478279 J Idle Energy 12397 86 eV Master Active Shutter Closed 06 36 37 PM Figure 2 13 BLU ICE SETUP TAB Beamline 4 2 2 is unique at the ALS in that we use a sagittally focused 2nd crystal in our monochromator This provides a spot shape that can be focused on a large range of detector distances with the entire beam hitting the focal point usually the sample A challenge during an energy change is keeping everything optimized for spot shape and maximum flux Specifically the beam focus and roll is subject to anticlastic bend and their values must be honed by staff on a somewhat regular basis Once these values are entered they tend to remain stable during the normal course of a user
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